write.psl: Write PSL file from dataframe or GRanges

In malnirav/hiReadsProcessor: Functions to process LM-PCR reads from 454/Illumina data

Description

Given a data frame or GRanges object, the function write a tab deliminated PSL file

Usage

write.psl(x, filename = "out.psl", header = FALSE, includeOtherCols = FALSE)

Arguments

x	data frame or GRanges object with required columns for psl file format.
filename	name for the output PSL file. Default is "out.psl"
header	include PSL header line. Default is FALSE.
includeOtherCols	nclude other non PSL specific columns from x in the output. Default is FALSE.

Value

name of the output PSL file

See Also

read.psl, blatSeqs, read.blast8, read.BAMasPSL, pslToRangedObject

Examples

data(psl)
pslFile <- tempfile()
write.psl(psl, filename = pslFile)

malnirav/hiReadsProcessor documentation built on July 29, 2021, 6:33 a.m.